Update ChangeLog for fix for Issue 669
added new sandbox scripts, collect-reads and slice-reads-by-coverage, into README
changelog update
Merge pull request #595 from ged-lab/cleanup/sandbox

Further cleanup of sandbox/ scripts.
Close open file handles in load-into-counting.py

We now use `with open(X) as y:` which automatically handles the closing
of files.
Add a tab-seperated output to load-into-counting

This adds a CLI flag to load-into-counting.py allowing it to output the
FPR, total number of distinct k-mers (cm-sketch occupancy) and input
files in a machine/R/excel readable format to save us from resorting to
regex hacks to pull this info out of out.kh.info etc.

I've also make the info files contain all files used as input.

I've also also added a test of the tsv creation behaviour.

Changes:
	modified:   scripts/load-into-counting.py:
			new cli flag, write all inputs to .info file
	modified:   tests/test_scripts.py:
			add test of the new cli flag
load-into-counting: Fix typo in "total kmers" line

Writing it to the info file had the wrong sentence.
load-into-counting: Less confusing info print line
load-in2-count: Add json/TSV machine readable info

This changes the CLI flag that enables machine readable info so that to
enalbe this behaviour, you give it an argument of either 'json' or
'tsv'. This allows for a user choice of a versioned, dat-friendly json
or something easy to whack into R and plot.
Add format version to load-in2-counting json info

Add a file format version key-val pair
Use argparse's choices param to validate arg

We now use the choices kwarg to parser.add_argument to validate the
---machine-readable-info argument, instead of manually checking it.

Also, updates the tests.

	modified:   scripts/load-into-counting.py
	modified:   tests/test_scripts.py
Update changelog with load-into-counting changes

	modified:   ChangeLog
load-in22-count: use new ht.n_unique_kmers method

New API feature in ChangeLog on 2014-11-06. Also solves merge
conflict (hopefully)

	modified:   scripts/load-into-counting.py
Change --machine-readable-info to --summary-info

This changes the overly long flag we added in PR #649 to be a little
shorter.
Fix broken test in test_scripts.py

Forgot to update the expected stderr after a rebase changed it.
	modified:   tests/test_scripts.py
Revert erroneous merge conflict resolution

Accidentally changed a few unrelated issues while fixing merge
conflcits. Reverted as asked to by @mr-c.

Also remove duplicated status line introduced in a similar manner.
	modified:   scripts/load-into-counting.py
Merge branch 'kdmurray91-feature/load-into-counting_tsv-output'
formatting fixes
Stop test from creating random file in ./

One of the tests for normalise-by-median in test_scripts.py created an
extra file in the current directory. This patch ensures that we manually
specify an output file.

	modified:   tests/test_scripts.py
Add test fix to ChangeLog

	modified:   ChangeLog